IR does change quite a bit between discharged and fully charged. there is really no right or wrong way to measure it but try to always measure packs in the same charge state if you want to be able to compare results. Same thing goes for temeperature.

Originally Posted by chuckinnc

If I had a 2S and 3S pack of the same current, would the 3S give better
(lower milliohm) reading?

No, if you are measuring total pack resistance then the 3s would be higher because the resistance of all cells is added together. If you are measuring individual cell resistance then it will be the same for 3s as 2s (or any other number of cells)

Originally Posted by chuckinnc

If I had 2S - 2000ma and a 2S - 4000ma would the higer
current pack give better reading?

Yes, you would expect the 4000mAh battery to have around half the IR as the 2000mAh battery.. Note that the capacity in mAh (Milliamp-Hours) is a measure of charge capacity, not current as such.